First, we filtered 7 ROIs with low signals of housekeeping genes which geometric mean are lower than 4.
Then we also calculated the geometric mean of IgG signals in each ROI.
According to the correlation between housekeeping and IgG background signal are concordant with each other.
We computed the signal-to-background ratio per target, which is simply each ROI’s data divided by its IgG geomean. And we removed 26 targets with lower signals than the control group in the ROIs.
We finally chose the housekeeping normalization for data normalization.
After the data normalization and the low targets removal, we tested the correlation between each ROIs.
We performed the comparisons in M12, F12, M3, and F3, within the Hip and Non_hip respectively. L vs. C LPE vs. L LPG vs. L LPG vs. LPE